I use a modified Vernier gauge (these are available from £7) with the external calipers ground off, this makes the ports inside the barrel very accessible.
This is the Inlet port height measured with my modified vernier caliper.

This picture shows my ground down caliper. Mine need to be re-calibrated by eye each time they are used, as I have removed the maximum amount of metal from the external part of the caliper. If I had left a small portion then it would be easier to zero the reading prior to using them. but access is better on small components as they are...
I think this makes it easier to get a good reading compared to using a steel ruler, and measuring transfers in the bore is far more accurate, IMO.
This is the gauge being use to measure an exhaust port on the same barrel.

